The genomic epidemiological database for global identification of microorganisms or global microbial identifier is a platform for storing

whole genome sequencing Whole genome sequencing (WGS), also known as full genome sequencing, complete genome sequencing, or entire genome sequencing, is the process of determining the entirety, or nearly the entirety, of the DNA sequence of an organism's genome at a s ...

data of

microorganisms A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is sometimes hyphenated (''micro-organism''), especially in olde ...

, for the identification of relevant

genes In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...

and for the comparison of

genomes In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding gen ...

to detect and track-and-trace

infectious disease An infection is the invasion of tissues by pathogens, their multiplication, and the reaction of host tissues to the infectious agent and the toxins they produce. An infectious disease, also known as a transmissible disease or communicable dise ...

outbreaks and emerging pathogens. The database holds two types of information: 1) genomic information of

, linked to, 2)

metadata Metadata is "data that provides information about other data", but not the content of the data, such as the text of a message or the image itself. There are many distinct types of metadata, including: * Descriptive metadata – the descriptive ...

of those microorganism such as

epidemiological Epidemiology is the study and analysis of the distribution (who, when, and where), patterns and determinants of health and disease conditions in a defined population. It is a cornerstone of public health, and shapes policy decisions and evidenc ...

details. The database includes all genera of microorganisms:

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...

viruses A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsky's 1 ...

, parasites and

fungi A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from ...

Technology

For genotyping of microorganisms for

medical diagnosis Medical diagnosis (abbreviated Dx, Dx, or Ds) is the process of determining which disease or condition explains a person's symptoms and signs. It is most often referred to as diagnosis with the medical context being implicit. The information re ...

, or other purposes, scientists may use a wide variety of

DNA profiling DNA profiling (also called DNA fingerprinting) is the process of determining an individual's DNA characteristics. DNA analysis intended to identify a species, rather than an individual, is called DNA barcoding. DNA profiling is a forensic tec ...

techniques, such as

polymerase chain reaction The polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies (complete or partial) of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it (or a part of it) t ...

pulsed-field gel electrophoresis Pulsed field gel electrophoresis is a technique used for the separation of large DNA molecules by applying to a gel matrix an electric field that periodically changes direction. Historical background Standard gel electrophoresis techniques for ...

multilocus sequence typing Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci, using DNA sequences of internal fragments of multiple housekeeping genes to characterize isolates of microbial species. The first MLST scheme ...

. A complication of this broad variety of techniques is the difficulty to standardize between techniques, laboratories and microorganisms, which may be overcome using the complete DNA code of the genome generated by whole genome sequencing. For straightforward diagnostic identification, the whole genome sequencing information of a microbiological sample is fed into a global genomic database and compared using BLAST procedures to the genomes already present in the database. In addition, whole genome sequencing data may be used to back calculate to the different pre-whole genome sequencing genotyping methods, so previous collected valuable information is not lost. For the global microbial identifier the genomic information is coupled to a wide spectrum of metadata about the specific microbial clone and includes important clinical and

information such as the global finding places, treatment options and antimicrobial resistance, making it a general microbiological identification tool. This makes personalized treatment of microbial disease possible as well as real-time tracing systems for global surveillance of

infectious diseases An infection is the invasion of tissues by pathogens, their multiplication, and the reaction of host tissues to the infectious agent and the toxins they produce. An infectious disease, also known as a transmissible disease or communicable dise ...

for

food safety Food safety (or food hygiene) is used as a scientific method/discipline describing handling, preparation, and storage of food in ways that prevent food-borne illness. The occurrence of two or more cases of a similar illness resulting from t ...

and serving

human health Health, according to the World Health Organization, is "a state of complete physical, mental and social well-being and not merely the absence of disease and infirmity".World Health Organization. (2006)''Constitution of the World Health Organiza ...

The initiative

The initiative for building the database arose in 2011 and when several preconditions were met: 1) whole genome sequencing has become mature and serious alternative for other genotyping techniques, 2) the price of whole genome sequencing has started falling dramatically and in some cases below the price of traditional identifications, 3) vast amounts of IT resources and a fast

Internet The Internet (or internet) is the global system of interconnected computer networks that uses the Internet protocol suite (TCP/IP) to communicate between networks and devices. It is a '' network of networks'' that consists of private, pub ...

have become available, and 4) there is the idea that via a cross sectoral and One Health approach infectious diseases may be better controlled. Starting the second millennium, many microbiological laboratories, as well as national health institutes, started genome sequencing projects for sequencing the infectious agents collections they had in their biobanks. Thereby generating private databases and sending model genomes to global nucleotide databases such as GenBank of the

National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The ...

or the nucleotide database of the

EMBL The European Molecular Biology Laboratory (EMBL) is an intergovernmental organization dedicated to molecular biology research and is supported by 27 member states, two prospect states, and one associate member state. EMBL was created in 1974 and ...

. This created a wealth of genomic information and independent databases for

eukaryotic Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacte ...

as well as prokaryotic genomes. The need to further integrate these databases and to harmonize data collection, and to link the genomic data to metadata for optimal prevention of infectious diseases, was generally recognized by the scientific community. In 2011, several infectious disease control centers and other organizations took the initiative of a series of international scientific- and policy-meetings, to develop a common platform and to better understand the potentials of an interactive microbiological genomic database. The first meeting was in Brussels, September 2011, followed by meetings in Washington (March 2012) and Copenhagen (February 2013). In addition to experts from around the globe, Intergovernmental Organizations have been included in the action, notably the

World Health Organization The World Health Organization (WHO) is a specialized agency of the United Nations responsible for international public health. The WHO Constitution states its main objective as "the attainment by all peoples of the highest possible level of h ...

and the

World Organization for Animal Health The World Organisation for Animal Health (WOAH), formerly the (OIE), is an intergovernmental organization coordinating, supporting and promoting animal disease control. Mission and status The main objective of the WOAH is to control epizoo ...

Development plan

A detailed roadmap for the development of the database was set up with the following general timeline: :2010 - 2012: Development of pilot systems. :2011 - 2013: International structural start-up, with the formation of an international core group, analysis of the present and future landscape to build the database, and diplomacy efforts to bring the relevant groups together. :2012 - 2016: Development of a robust IT-backbone for the database, and development of novel genome analysis algorithms and software. :2017 - 2020: Construction of a global solution, including the creation of networks and regional hubs.

Steering committee

Current members: * Eric Brown,

Food and Drug Administration The United States Food and Drug Administration (FDA or US FDA) is a List of United States federal agencies, federal agency of the United States Department of Health and Human Services, Department of Health and Human Services. The FDA is respon ...

, USA * Amy Cawthorne,

, Switzerland * Jørgen Schlundt,

Nanyang Technological University The Nanyang Technological University (NTU) is a national research university in Singapore. It is the second oldest autonomous university in the country and is considered as one of the most prestigious universities in the world by various inte ...

, Singapore. *

David J. Lipman David J. Lipman is an American biologist who from 1989 to 2017 was the director of the National Center for Biotechnology Information (NCBI) at the National Institutes of Health. NCBI is the home of GenBank, the U.S. node of the International Sequ ...

, USA. * Alisdair Wotherspoon,

Food Standards Agency , type = Non-ministerial government department , nativename = , nativename_a = , nativename_r = , logo = Food Standards Agency.svg , logo_width = , logo_caption = , seal = , seal_width = , seal_caption = , picture = , picture_width = , ...

, United Kingdom. * Pathom Sawanpanyalert, Ministry of Public Health, Thailand. * David Heyman, Health Protection Agency, United Kingdom. *

Marion Koopmans Maria Petronella Gerarda Koopmans (born 21 September 1956) is a Dutch virologist who is Head of the Erasmus MC Department of Viroscience. Her research considers emerging infectious diseases, noroviruses and veterinary medicine. In 2018 she was aw ...

Erasmus University Medical Center Erasmus University Medical Center (Erasmus MC or EMC) based in Rotterdam, Netherlands, affiliated with Erasmus University and home to its faculty of medicine, is the largest and one of the most authoritative scientific University Medical Centers in ...

Netherlands National Institute for Public Health and the Environment The National Institute for Public Health and the Environment ( nl, Rijksinstituut voor Volksgezondheid en Milieu or simply RIVM) is a Dutch research institute that is an independent agency of the Ministry of Health, Welfare and Sport. RIVM perfo ...

. * Masami T. Takeuchi,

Food and Agriculture Organization The Food and Agriculture Organization of the United Nations (FAO)french: link=no, Organisation des Nations unies pour l'alimentation et l'agriculture; it, Organizzazione delle Nazioni Unite per l'Alimentazione e l'Agricoltura is an intern ...

* Vincenco Caporale, World Organization of Animal Health Former members: * Steven M. Musser,

, USA. * Angelik Tritscher,

, Switzerland.

References

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External links